To mitigate the asynchronous ICI (Inter-Cell Interference), SCM (Spatial Covariance Matrix) of the asynchronous ICI plus background noise should be accurately estimated for MIMO-OFDMA (Multiple-input Multiple-output-Orthogonal Frequency Division Multiple Access) system. Generally, it is assumed that the SCM of the asynchronous ICI plus background noise is estimated by using training symbols. However, it is difficult to measure the interference statistics for a long time and considering that training symbols are not appropriate for OFDMA system such as LTE (3GPP Long Term Evolution). Therefore, noise reduction method is required to improve the estimation accuracy. Although the conventional time-domain low-pass type weighting method can be effective for noise reduction, it causes significant estimation error due to the spectral leakage in practical OFDM system. Therefore, we propose a time-domain sinc type weighing method which can not only reduce noise effectively minimizing estimation error caused by the spectral leakage but also can be implemented using frequency-domain weighted moving average filter easily. We also consider the iterative CFR (Channel Frequency Response) and SCM estimation method which can effectively reduce the estimation error of both CFR and SCM, and improve the performance for LTE system. By using computer simulation, we show that the proposed method can provide up to 2.5dB SIR (Signal to Interference Ratio) gain compared with the conventional method, and verify that the proposed method is attractive and suitable for implementation with stable operation.